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- PDB-5y6d: VIM-2 metallo-beta-lactamase in complex with (R)-2-(4-fluoropheny... -

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Basic information

Entry
Database: PDB / ID: 5y6d
TitleVIM-2 metallo-beta-lactamase in complex with (R)-2-(4-fluorophenyl)-2-((S)-3-mercapto-2-methylpropanamido)acetic acid (compound 11)
ComponentsBeta-lactamase class B VIM-2
KeywordsHYDROLASE / Beta-lactamase / Metallo-beta-lactamase VIM-2 / VIM-2
Function / homology
Function and homology information


beta-lactamase / hydrolase activity / metal ion binding
Similarity search - Function
: / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-8PL / FORMIC ACID / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsLi, G.-B.
CitationJournal: Eur J Med Chem / Year: 2018
Title: ((S)-3-Mercapto-2-methylpropanamido)acetic acid derivatives as metallo-beta-lactamase inhibitors: Synthesis, kinetic and crystallographic studies.
Authors: Liu, S. / Jing, L. / Yu, Z.-J. / Wu, C. / Zheng, Y. / Zhang, E. / Chen, Q. / Yu, Y. / Guo, L. / Wu, Y. / Li, G.-B.
History
DepositionAug 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2018Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase class B VIM-2
B: Beta-lactamase class B VIM-2
C: Beta-lactamase class B VIM-2
D: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,43818
Polymers98,7184
Non-polymers1,72014
Water6,972387
1
A: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1936
Polymers24,6791
Non-polymers5145
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-22 kcal/mol
Surface area9160 Å2
MethodPISA
2
B: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0824
Polymers24,6791
Non-polymers4023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9330 Å2
MethodPISA
3
C: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0824
Polymers24,6791
Non-polymers4023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9320 Å2
MethodPISA
4
D: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0824
Polymers24,6791
Non-polymers4023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.030, 39.832, 133.841
Angle α, β, γ (deg.)90.000, 124.560, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Beta-lactamase class B VIM-2 / BlaVIM-2 / Metallo beta lactamase VIM-2 / Metallo beta-lactamase / Metallo-beta lactamase protein / ...BlaVIM-2 / Metallo beta lactamase VIM-2 / Metallo beta-lactamase / Metallo-beta lactamase protein / Metallo-beta-lactamase VIM-2 / VIM-2 class B beta-lactamase / VIM-2 class B metallo b-lactamase / VIM-2 metallo beta-lactamase / VIM-2 type metallo-beta-lactamase


Mass: 24679.439 Da / Num. of mol.: 4 / Fragment: UNP residues 32-262
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: blaVIM-2, bla vim-2, bla-VIM-2, blasVIM-2, blaVIM2, blm, VIM-2, vim-2, PAERUG_P32_London_17_VIM_2_10_11_06255
Plasmid: opinf vector based / Details (production host): Plasmid derived / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q9K2N0
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-8PL / (2R)-2-(4-fluorophenyl)-2-[[(2S)-2-methyl-3-sulfanyl-propanoyl]amino]ethanoic acid / (R)-2-(4-fluorophenyl)-2-((S)-3-mercapto-2-methylpropanamido)acetic acid


Mass: 271.308 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H14FNO3S
#4: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 387 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1M Magnesium Formate, 21%-27% (v/v) Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 90510 / % possible obs: 99.4 % / Redundancy: 6.4 % / Biso Wilson estimate: 18.86 Å2 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.044 / Rrim(I) all: 0.113 / Χ2: 0.958 / Net I/σ(I): 4.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.76-1.794.30.62337190.6860.320.7040.90191
1.79-1.825.50.5840530.7730.2660.6410.91899.2
1.82-1.866.10.52440590.830.230.5730.91899.9
1.86-1.96.50.46141320.8630.1950.5020.95699.9
1.9-1.946.60.39840110.8950.1670.4320.944100
1.94-1.986.60.33841020.9290.1420.3670.96199.8
1.98-2.036.20.28440600.9390.1230.310.96399.8
2.03-2.096.40.24841040.9540.1060.2710.97199.9
2.09-2.156.90.23240860.9620.0950.2520.969100
2.15-2.226.90.20640950.9670.0840.2230.971100
2.22-2.36.70.19140670.9740.0790.2070.97599.7
2.3-2.396.60.16640940.9780.0690.180.965100
2.39-2.56.20.14441240.980.0620.1570.95399.9
2.5-2.636.70.13441360.9830.0560.1450.975100
2.63-2.796.80.11640920.9880.0480.1250.97100
2.79-3.016.80.10141270.990.0410.1090.961100
3.01-3.316.30.0841510.9910.0340.0870.99399.9
3.31-3.796.90.06941300.9950.0280.0751.04399.9
3.79-4.786.50.05842030.9960.0240.0631.009100
4.78-506.40.05543530.9960.0230.060.811100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.54 Å45.74 Å
Translation6.54 Å45.74 Å

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHASER2.6.0phasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LCA

5lca


Resolution: 2.1→45.736 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.94
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2188 2253 2.49 %
Rwork0.1617 --
obs0.1632 90510 96.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 109 Å2 / Biso mean: 23.2658 Å2 / Biso min: 5.82 Å2
Refinement stepCycle: final / Resolution: 2.1→45.736 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6899 0 84 389 7372
Biso mean--25.91 25.34 -
Num. residues----922
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0147175
X-RAY DIFFRACTIONf_angle_d1.0689768
X-RAY DIFFRACTIONf_chiral_restr0.0591124
X-RAY DIFFRACTIONf_plane_restr0.0081280
X-RAY DIFFRACTIONf_dihedral_angle_d13.5834119
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.14570.21371200.17154576469681
2.1457-2.19560.2931260.17594979510587
2.1956-2.25050.29671340.17625115524990
2.2505-2.31130.17241360.1765353548994
2.3113-2.37930.24141430.17325572571597
2.3793-2.45610.2271420.17125592573498
2.4561-2.54390.26031450.16615673581899
2.5439-2.64580.21751450.165357265871100
2.6458-2.76620.20491450.164456785823100
2.7662-2.9120.24941400.163257135853100
2.912-3.09440.21491450.169157455890100
3.0944-3.33320.2461470.161657435890100
3.3332-3.66850.23211480.149456735821100
3.6685-4.19910.18431430.14557075850100
4.1991-5.28910.18891430.13856995842100
5.2891-45.74660.20071510.184257135864100

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